UCSF

RNA switches are key regulators of gene expression in bacteria, yet very few have been described and characterized in Metazoa. Here, we present an integrative computational and experimental approach to systematically annotate functional RNA structural switches genome-wide. By applying this approach to the human transcriptome, we discovered 245 putative RNA switches. Among these, we further characterized and functionally dissected a previously unknown RNA switch in the 3’UTR of the RORC gene. In vivo DMS-MaPseq complemented by cryogenic electron microscopy confirmed the existence of this element as an ensemble of two alternative functional conformations. We then used a genome-wide CRISRPi screen to identify the trans factors that mediate gene expression through this RNA structural switch. We discovered that the nonsense-mediated mRNA decay pathway acts on this element in a conformation-specific manner. Our findings suggest that RNA structural switches may play an important, yet underappreciated role, in shaping the gene expression landscape of the cell in eukaryotes.RNA-binding proteins (RBPs) are multifunctional regulators of gene expression with complex and context-dependent mechanisms of action. The underlying regulatory grammar that underlies RBP-mediated functions remains largely unexplored. Here, we developed and applied a multi-omic data integration platform to systematically decipher the context-specific functions of RBPs. We used in vivo proximity-dependent biotinylation (BioID) analysis of 50 human RBPs to generate a comprehensive map of major RBP neighborhoods. In parallel, we took advantage of CRISPR-interference with single-cell RNA-seq read-out (CROP-seq) to effectively capture the overall transcriptomic response downstream of each RBP knockdown. By integrating these physical and functional interaction data with the ENCODE transcriptome-wide atlas of RBP binding from eCLIP assays, we generated a map of RBP functional interaction. The resulting map captures well-studied post-transcriptional pathways and reveals novel RPB-mediated regulatory functions. Here, we report the validation of context-specific functions for several RBPs using biochemical and genetic approaches. We showed that TAF15 controls splicing, translation, and stability for distinct and largely independent RNA regulons. Similarly, we demonstrated that ZNF800 and QKI play non-canonical roles in both transcriptional and post-transcriptional regulation. Taken together, our integrative map reveals that each RBP may participate in multiple post-transcriptional regulatory modules, each with their own target regulon and regulatory function. Deciphering these complex modes of function and interaction are the first step towards a better understanding of post-transcriptional control in health and disease.